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- EMDB-30799: 9.4A reconstruction of Tokyovirus using 1,000 KV JEOL JEM-1000EES... -

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Basic information

Entry
Database: EMDB / ID: EMD-30799
Title9.4A reconstruction of Tokyovirus using 1,000 KV JEOL JEM-1000EES, varies from 7.7A reconstruction only by post-processing mask
Map data9.4A postproc map of Tokyovirus, acquired on a JEOL JEM-1000EES HVEM. Map differs from 7.7A and 8.7A map only by post-process mask applied (soft spherical)
Sample
  • Virus: Tokyovirus A1
Biological speciesTokyovirus A1
Methodsingle particle reconstruction / cryo EM / Resolution: 9.4 Å
AuthorsBurton-Smith R / Murata K
Funding support Japan, 1 items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP19H04845 Japan
CitationJournal: Microscopy (Oxf) / Year: 2021
Title: Cryo-electron microscopy of the giant viruses.
Authors: Raymond N Burton-Smith / Kazuyoshi Murata /
Abstract: High-resolution study of the giant viruses presents one of the latest challenges in cryo-electron microscopy (EM) of viruses. Too small for light microscopy but too large for easy study at high ...High-resolution study of the giant viruses presents one of the latest challenges in cryo-electron microscopy (EM) of viruses. Too small for light microscopy but too large for easy study at high resolution by EM, they range in size from ∼0.2 to 2 μm from high-symmetry icosahedral viruses, such as Paramecium burseria Chlorella virus 1, to asymmetric forms like Tupanvirus or Pithovirus. To attain high resolution, two strategies exist to study these large viruses by cryo-EM: first, increasing the acceleration voltage of the electron microscope to improve sample penetration and overcome the limitations imposed by electro-optical physics at lower voltages, and, second, the method of 'block-based reconstruction' pioneered by Michael G. Rossmann and his collaborators, which resolves the latter limitation through an elegant leveraging of high symmetry but cannot overcome sample penetration limitations. In addition, more recent advances in both computational capacity and image processing also yield assistance in studying the giant viruses. Especially, the inclusion of Ewald sphere correction can provide large improvements in attainable resolutions for 300 kV electron microscopes. Despite this, the study of giant viruses remains a significant challenge.
History
DepositionDec 17, 2020-
Header (metadata) releaseDec 22, 2021-
Map releaseDec 22, 2021-
UpdateDec 22, 2021-
Current statusDec 22, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30799.png

Downloads & links

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Map

FileDownload / File: emd_30799.map.gz / Format: CCP4 / Size: 6.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation9.4A postproc map of Tokyovirus, acquired on a JEOL JEM-1000EES HVEM. Map differs from 7.7A and 8.7A map only by post-process mask applied (soft spherical)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.91 Å/pix.
x 1200 pix.
= 3494.4 Å		2.91 Å/pix.
x 1200 pix.
= 3494.4 Å		2.91 Å/pix.
x 1200 pix.
= 3494.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.912 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006 / Movie #1: 0.006
Minimum - Maximum-0.016310742 - 0.01602627
Average (Standard dev.)-7.896214e-05 (±0.0013395381)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120012001200
Spacing120012001200
CellA=B=C: 3494.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.9122.9122.912
M x/y/z120012001200
origin x/y/z0.0000.0000.000
length x/y/z3494.4003494.4003494.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS120012001200
D min/max/mean-0.0160.016-0.000

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Supplemental data

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Sample components

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Entire : Tokyovirus A1

EntireName: Tokyovirus A1
Components
  • Virus: Tokyovirus A1

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Supramolecule #1: Tokyovirus A1

SupramoleculeName: Tokyovirus A1 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 1826170 / Sci species name: Tokyovirus A1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Acanthamoeba castellanii (eukaryote)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL 1000EES
DetailsMicroscope used was actually JEOL JEM-1000EES, however this is currently not available in the list of Microscope models.
Image recordingFilm or detector model: GATAN K2 IS (4k x 4k) / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 1000 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm

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Image processing

Particle selectionNumber selected: 1529
Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1182
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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